From d598f71349d0dbb7f88b13ba5bd9de739bc6a8d3 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Fri, 11 Jun 2021 20:25:00 +0100 Subject: [PATCH 001/100] add UTF8 charset to template meta tag, fixes weird symbol rendering --- data/templates/single_template.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/data/templates/single_template.html b/data/templates/single_template.html index c863783e..b8157c43 100644 --- a/data/templates/single_template.html +++ b/data/templates/single_template.html @@ -1,11 +1,11 @@ - + --> + + + + + + + + + + + + + + --> - - - - - - + @@ -150,7 +166,7 @@

Per gene coverage summary


- +
@@ -235,6 +251,8 @@

Coverage of Known Variants

$('#fullPlots').DataTable( { data: data, deferRender: true, + pageResize: true, + info: false, scrollY: "750px", scrollCollapse: true, scroller: true, @@ -261,11 +279,6 @@

Coverage of Known Variants

] }); }); - // setTimeout( function () { - // // Make the example container visible and recalculate the scroller sizes - // document.getElementById('#fullPlots').style.display = "block"; - // oTable.fnSettings().oScroller.fnMeasure(); - // }, 3000 ); From ffa5d9844734970320f87cf9a37e4e764b3b08e7 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Mon, 21 Jun 2021 12:52:47 +0100 Subject: [PATCH 015/100] increase plot size --- bin/coverage_report_single.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/coverage_report_single.py b/bin/coverage_report_single.py index c07db7fe..c4b6ea99 100644 --- a/bin/coverage_report_single.py +++ b/bin/coverage_report_single.py @@ -253,7 +253,7 @@ def all_gene_plots(self, raw_coverage): # make subplot grid size of no. of exons, height variable # splits large genes to several rows and maintains height - height = math.ceil(len(exons) / 30) * 4 + height = math.ceil(len(exons) / 30) * 4.5 fig = plt.figure(figsize=(30, height)) # generate grid with space for each exon From ae46474a542a7f9cf4ebce058bab9a27b91ed341 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Mon, 21 Jun 2021 13:01:12 +0100 Subject: [PATCH 016/100] improve plot labels --- bin/coverage_report_single.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/bin/coverage_report_single.py b/bin/coverage_report_single.py index c4b6ea99..2f3849e5 100644 --- a/bin/coverage_report_single.py +++ b/bin/coverage_report_single.py @@ -330,7 +330,12 @@ def all_gene_plots(self, raw_coverage): xlab = str( exon_cov["exon_end"].iloc[0] - exon_cov["exon_start"].iloc[0] - ) + "\nbp" + ) + " bp" + + if len(exons) > 20: + # drop bp to new line for better spacing + xlab = xlab.replace("bp", "\nbp") + axs[count].title.set_text(exon) axs[count].set_xlabel(xlab, fontsize=13) From 2fa5c66bcedf246f02540a6f612dae388eeeb1fe Mon Sep 17 00:00:00 2001 From: Jethro Date: Wed, 23 Jun 2021 18:26:28 +0100 Subject: [PATCH 017/100] changes to accomdate moving plotly functionality to JS function, low exon data passed out in array and directly rendered with datatables & plotly in html --- bin/coverage_report_single.py | 106 ++++++++++++++------- data/templates/single_template.html | 139 +++++++++++++++++++++++++++- 2 files changed, 208 insertions(+), 37 deletions(-) diff --git a/bin/coverage_report_single.py b/bin/coverage_report_single.py index 463a9f10..afb1dac3 100644 --- a/bin/coverage_report_single.py +++ b/bin/coverage_report_single.py @@ -103,6 +103,7 @@ def low_exon_plot(self, low_raw_cov): low_raw_cov["cov_end"] + low_raw_cov["cov_start"]) / 2 )) + """ # set no. rows to no. of plots / no of columns to define grid columns = 4 rows = math.ceil(len(genes) / 4) @@ -120,13 +121,19 @@ def low_exon_plot(self, low_raw_cov): # counter for grid row_no = 1 col_no = 1 + """ + low_exon_plots = [] for gene in genes: # make plot for each gene / exon + """ if row_no // 5 == 1: # counter for grid, gets to 5th entry & starts new row col_no += 1 row_no = 1 + """ + gene_data = [] + fig = go.Figure() # get rows for current gene and exon exon_cov = low_raw_cov.loc[( @@ -176,48 +183,77 @@ def low_exon_plot(self, low_raw_cov): # info field for hovering on plot line label = 'position: %{x}
coverage: %{y}' - # generate plot and threshold line to display - if sum(exon_cov_unbinned["cov"]) != 0: - plot = go.Scatter( - x=exon_cov_unbinned["cov_start"], y=exon_cov_unbinned["cov"], - mode="lines", - hovertemplate=label - ) - else: - # if any plots have no coverage, just display empty plot - # very hacky way by making data point transparent but - # ¯\_(ツ)_/¯ - plot = go.Scatter( - x=exon_cov_unbinned["cov_start"], y=exon_cov_unbinned["cov"], - mode="markers", marker={"opacity": 0} - ) - - threshold_line = go.Scatter( - x=xval, y=yval, hoverinfo='skip', mode="lines", - line=dict(color='rgb(205, 12, 24)', width=1) - ) + # # generate plot and threshold line to display + # if sum(exon_cov_unbinned["cov"]) != 0: + # plot = fig.add_trace(go.Scatter( + # x=exon_cov_unbinned["cov_start"], y=exon_cov_unbinned["cov"], + # mode="lines", + # hovertemplate=label + # )) + # else: + # # if any plots have no coverage, just display empty plot + # # very hacky way by making data point transparent but + # # ¯\_(ツ)_/¯ + # plot = fig.add_trace(go.Scatter( + # x=exon_cov_unbinned["cov_start"], y=exon_cov_unbinned["cov"], + # mode="markers", marker={"opacity": 0} + # )) + + # threshold_line = fig.add_trace(go.Scatter( + # x=xval, y=yval, hoverinfo='skip', mode="lines", + # line=dict(color='rgb(205, 12, 24)', width=1) + # )) # add to subplot grid - fig.add_trace(plot, col_no, row_no) - fig.add_trace(threshold_line, col_no, row_no) + # fig.add_trace(plot, col_no, row_no) + # fig.add_trace(threshold_line, col_no, row_no) - row_no = row_no + 1 + # row_no = row_no + 1 # set height of grid by no. rows and scale value of 325 - height = (rows * 300) + 150 - - # update plot formatting - fig.update_xaxes(nticks=3, ticks="", showgrid=True, tickformat=',d') - fig.update_yaxes(title='coverage', title_standoff=0) - fig.update_xaxes(title='exon position', color='#FFFFFF') - fig["layout"].update( - height=height, showlegend=False, margin=dict(l=50, r=0) - ) + # height = (rows * 300) + 150 + + + + # update plot formatting + # fig.update_xaxes(nticks=3, ticks="", showgrid=True, tickformat=',d') + # fig.update_yaxes(title='coverage', title_standoff=0) + # fig.update_xaxes(title='exon position', color='#FFFFFF') + # fig["layout"].update( + # showlegend=False, margin=dict(l=50, r=0), + # ) + + # # write plots to html string + # fig = fig.to_html(full_html=False) + + # # print(fig) + # print(len(fig.encode('utf-8')) / 1024 / 1024) + + if sum(exon_cov_unbinned["cov"]) == 0: + continue + + x_vals = exon_cov_unbinned['cov_start'].tolist() + y_vals = exon_cov_unbinned['cov'].tolist() + title = f"[{gene[0]} exon {gene[1]}]" + + # print(x_vals) + # print(y_vals) + # print(title) + + gene_data.append(title) + gene_data.append(x_vals) + gene_data.append(y_vals) + + for i in range(0, 10): + low_exon_plots.append(gene_data) + + # print(low_exon_plots) - # write plots to html string - fig = fig.to_html(full_html=False) + # print(len(low_exon_plots)) + # print(len(low_exon_plots[0])) + # sys.exit() - return fig + return low_exon_plots def all_gene_plots(self, raw_coverage): diff --git a/data/templates/single_template.html b/data/templates/single_template.html index c863783e..51a6afb4 100644 --- a/data/templates/single_template.html +++ b/data/templates/single_template.html @@ -2,6 +2,17 @@ + + + + + + + + + + + @@ -133,10 +161,16 @@

Exons with sub-optimal coverage

an interactive window on hovering, showing the coverage at that current base.
The top right also contains a toolbar, with functions such as panning and zooming. - -



-
+ +
+ + + + + + +







@@ -223,119 +257,146 @@

Coverage of Known Variants

- From a2e66e457208b96ee5f05e5d290e03d24253f219 Mon Sep 17 00:00:00 2001 From: Jethro Date: Sun, 27 Jun 2021 00:48:31 +0100 Subject: [PATCH 019/100] fix sorting in low exon plot area --- data/templates/single_template.html | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/data/templates/single_template.html b/data/templates/single_template.html index 12b14e72..e50329fd 100644 --- a/data/templates/single_template.html +++ b/data/templates/single_template.html @@ -257,6 +257,7 @@

Coverage of Known Variants

+ - - - \ No newline at end of file From 4249c65793e199c549811589cca4d917587d4343 Mon Sep 17 00:00:00 2001 From: Jethro Date: Sun, 27 Jun 2021 00:52:21 +0100 Subject: [PATCH 020/100] tidy up low_exon_plot() to remove old code --- bin/coverage_report_single.py | 88 +---------------------------------- 1 file changed, 2 insertions(+), 86 deletions(-) diff --git a/bin/coverage_report_single.py b/bin/coverage_report_single.py index 12f086c7..cade212b 100644 --- a/bin/coverage_report_single.py +++ b/bin/coverage_report_single.py @@ -103,37 +103,9 @@ def low_exon_plot(self, low_raw_cov): low_raw_cov["cov_end"] + low_raw_cov["cov_start"]) / 2 )) - """ - # set no. rows to no. of plots / no of columns to define grid - columns = 4 - rows = math.ceil(len(genes) / 4) - - # variable height depeendent on no. of plots - v_space = (1 / rows) * 0.25 - - # define grid to add plots to - fig = make_subplots( - rows=rows, cols=columns, print_grid=False, - horizontal_spacing=0.04, vertical_spacing=v_space, - subplot_titles=plot_titles - ) - - # counter for grid - row_no = 1 - col_no = 1 - """ - low_exon_plots = [] + low_exon_plots = [] # array to add string data of plots to for gene in genes: - # make plot for each gene / exon - """ - if row_no // 5 == 1: - # counter for grid, gets to 5th entry & starts new row - col_no += 1 - row_no = 1 - """ - fig = go.Figure() - # get rows for current gene and exon exon_cov = low_raw_cov.loc[( low_raw_cov["gene"] == gene[0] @@ -171,63 +143,6 @@ def low_exon_plot(self, low_raw_cov): pos_row, ignore_index=True ) - # build list of first and last point for threshold line - xval = [x for x in range( - exon_cov_unbinned["cov_start"].iloc[0], - exon_cov_unbinned["cov_end"].iloc[-1] - )] - xval = xval[::len(xval) - 1] - yval = [self.threshold] * 2 - - # info field for hovering on plot line - label = 'position: %{x}
coverage: %{y}' - - # # generate plot and threshold line to display - # if sum(exon_cov_unbinned["cov"]) != 0: - # plot = fig.add_trace(go.Scatter( - # x=exon_cov_unbinned["cov_start"], y=exon_cov_unbinned["cov"], - # mode="lines", - # hovertemplate=label - # )) - # else: - # # if any plots have no coverage, just display empty plot - # # very hacky way by making data point transparent but - # # ¯\_(ツ)_/¯ - # plot = fig.add_trace(go.Scatter( - # x=exon_cov_unbinned["cov_start"], y=exon_cov_unbinned["cov"], - # mode="markers", marker={"opacity": 0} - # )) - - # threshold_line = fig.add_trace(go.Scatter( - # x=xval, y=yval, hoverinfo='skip', mode="lines", - # line=dict(color='rgb(205, 12, 24)', width=1) - # )) - - # add to subplot grid - # fig.add_trace(plot, col_no, row_no) - # fig.add_trace(threshold_line, col_no, row_no) - - # row_no = row_no + 1 - - # set height of grid by no. rows and scale value of 325 - # height = (rows * 300) + 150 - - - - # update plot formatting - # fig.update_xaxes(nticks=3, ticks="", showgrid=True, tickformat=',d') - # fig.update_yaxes(title='coverage', title_standoff=0) - # fig.update_xaxes(title='exon position', color='#FFFFFF') - # fig["layout"].update( - # showlegend=False, margin=dict(l=50, r=0), - # ) - - # # write plots to html string - # fig = fig.to_html(full_html=False) - - # # print(fig) - # print(len(fig.encode('utf-8')) / 1024 / 1024) - if sum(exon_cov_unbinned["cov"]) == 0: continue @@ -236,6 +151,7 @@ def low_exon_plot(self, low_raw_cov): y_vals = str(exon_cov_unbinned['cov'].tolist()).strip('[]') title = f"{gene[0]} exon {gene[1]}" + # format string to pass values to report gene_data = ( f"""'
{title},{x_vals},{y_vals}
'""" ) From 043d634e8e70bd31ea17d543aa9d5a4de2111a59 Mon Sep 17 00:00:00 2001 From: Jethro Date: Sun, 27 Jun 2021 11:58:42 +0100 Subject: [PATCH 021/100] formatting and comments --- bin/coverage_report_single.py | 11 ++++++----- data/templates/single_template.html | 5 +---- 2 files changed, 7 insertions(+), 9 deletions(-) diff --git a/bin/coverage_report_single.py b/bin/coverage_report_single.py index cade212b..8229eced 100644 --- a/bin/coverage_report_single.py +++ b/bin/coverage_report_single.py @@ -160,7 +160,7 @@ def low_exon_plot(self, low_raw_cov): # low_exon_plots.append(gene_data) low_exon_plots.append(gene_data) - + low_exon_plots = ','.join(low_exon_plots) return low_exon_plots @@ -350,6 +350,7 @@ def summary_gene_plot(self, cov_summary): genes100pct = len(summary_data.iloc[:-100]) summary_data = summary_data.iloc[-100:] + # generate the plot plt.bar( summary_data["gene"], [int(x) for x in summary_data[self.threshold]], @@ -357,8 +358,8 @@ def summary_gene_plot(self, cov_summary): ) if genes100pct is not None: - genes100pct = str(genes100pct) # more than 100 genes, add title inc. 100% covered not shown + genes100pct = str(genes100pct) axs.set_title( r"$\bf{" + genes100pct + "}$" + " genes covered 100% at " + r"$\bf{" + self.threshold + "}$" + @@ -392,13 +393,13 @@ def summary_gene_plot(self, cov_summary): plt.legend( handles=[green, orange, red], loc='upper center', - bbox_to_anchor=(0.5, -0.1), - fancybox=True, shadow=True, ncol=12, fontsize=12 + bbox_to_anchor=(0.5, -0.15), + fancybox=True, shadow=True, ncol=12, fontsize=14 ) vals = np.arange(0, 110, 10).tolist() plt.yticks(vals, vals) - axs.tick_params(axis='both', which='major', labelsize=8) + axs.tick_params(axis='both', which='major', labelsize=12) plt.xlabel("") plt.ylabel("% coverage ({})".format(self.threshold), fontsize=11) diff --git a/data/templates/single_template.html b/data/templates/single_template.html index e50329fd..f15cf70b 100644 --- a/data/templates/single_template.html +++ b/data/templates/single_template.html @@ -25,7 +25,7 @@ body { padding-top: 100; padding-bottom: 150; - width: 90%; + width: 85%; margin-left: auto; margin-right: auto; font-size:18px; @@ -76,8 +76,6 @@ /* low exon plot styling */ #plot_container { - /* padding: 10px; */ - /* margin: 10px; */ width: 100%; } .sub_plot { @@ -171,7 +169,6 @@

Exons with sub-optimal coverage

-







From 6c153d1e5c5a1596e94edd10996f97cd31eda31c Mon Sep 17 00:00:00 2001 From: Jethro Date: Sun, 27 Jun 2021 12:01:08 +0100 Subject: [PATCH 022/100] update docstring --- bin/coverage_report_single.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/bin/coverage_report_single.py b/bin/coverage_report_single.py index 8229eced..6e28a922 100644 --- a/bin/coverage_report_single.py +++ b/bin/coverage_report_single.py @@ -66,8 +66,7 @@ def img2str(self, plt): def low_exon_plot(self, low_raw_cov): """ - Plot bp coverage of exon, used for those where coverage is given - threshold + Generate array of low exon plot values to pass into report Args: - low_raw_cov (df): df of raw coverage for exons with low @@ -75,7 +74,7 @@ def low_exon_plot(self, low_raw_cov): - threshold (int): defined threshold level (default: 20) Returns: - - fig (figure): plots of low coverage regions + - low_exon_plots (list): list of lists with values for plots """ print("Generating plots of low covered regions") @@ -156,9 +155,6 @@ def low_exon_plot(self, low_raw_cov): f"""'
{title},{x_vals},{y_vals}
'""" ) - # for i in range(0, 10): - # low_exon_plots.append(gene_data) - low_exon_plots.append(gene_data) low_exon_plots = ','.join(low_exon_plots) From e9226d2f13425c7a3c003f1d2ec7184037d3e700 Mon Sep 17 00:00:00 2001 From: Jethro Date: Sun, 27 Jun 2021 12:19:03 +0100 Subject: [PATCH 023/100] low exon plot formatting --- bin/coverage_report_single.py | 7 ++++--- data/templates/single_template.html | 2 +- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/bin/coverage_report_single.py b/bin/coverage_report_single.py index 6e28a922..6ae4f4cd 100644 --- a/bin/coverage_report_single.py +++ b/bin/coverage_report_single.py @@ -74,7 +74,7 @@ def low_exon_plot(self, low_raw_cov): - threshold (int): defined threshold level (default: 20) Returns: - - low_exon_plots (list): list of lists with values for plots + - low_exon_plots (str): list of plot values in div tags """ print("Generating plots of low covered regions") @@ -93,8 +93,6 @@ def low_exon_plot(self, low_raw_cov): # sort list of genes/exons by gene and exon genes = sorted(genes, key=lambda element: (element[0], element[1])) - plot_titles = [str(x[0]) + " exon: " + str(int(x[1])) for x in genes] - low_raw_cov["exon_len"] =\ low_raw_cov["exon_end"] - low_raw_cov["exon_start"] @@ -157,6 +155,9 @@ def low_exon_plot(self, low_raw_cov): low_exon_plots.append(gene_data) + for i in range(30): + low_exon_plots.append(gene_data) + low_exon_plots = ','.join(low_exon_plots) return low_exon_plots diff --git a/data/templates/single_template.html b/data/templates/single_template.html index f15cf70b..5f79bb81 100644 --- a/data/templates/single_template.html +++ b/data/templates/single_template.html @@ -315,7 +315,7 @@

Coverage of Known Variants

var table = $('#low_plots_grid').DataTable({ data: data, deferRender: true, - scrollY: "75vh", + scrollY: "85vh", scrollX: true, "searching": false, "lengthMenu": [[15, 30, 60, -1], [15, 30, 60, "All"]], From a5d95ba7f23268a4ad2ac75ebc47e43b6a713191 Mon Sep 17 00:00:00 2001 From: Jethro Date: Sun, 27 Jun 2021 12:30:27 +0100 Subject: [PATCH 024/100] comments for datatables/plotly script --- data/templates/single_template.html | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/data/templates/single_template.html b/data/templates/single_template.html index 5f79bb81..b5682a3e 100644 --- a/data/templates/single_template.html +++ b/data/templates/single_template.html @@ -256,6 +256,15 @@

Coverage of Known Variants

+ + + + + + + + + - - - - - @@ -151,7 +172,15 @@

Exons with <100% coverage at $threshold

an interactive window on hovering, showing the coverage at that current base.
The top right also contains a toolbar, with functions such as panning and zooming. - $low_cov_plots +



+ + + + + + + +



From a2c7bbe590028a49b58c75e9f8bdefc603fd73a4 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Tue, 29 Jun 2021 13:54:54 +0100 Subject: [PATCH 050/100] move copy to clipboard function to head --- data/templates/single_template.html | 28 +++++++++++++++------------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/data/templates/single_template.html b/data/templates/single_template.html index cfbb6a01..bfb18cc5 100644 --- a/data/templates/single_template.html +++ b/data/templates/single_template.html @@ -13,6 +13,19 @@ + + + + @@ -397,7 +394,7 @@

Coverage of Known Variants

var table = $('#low_plots_grid').DataTable({ data: data, deferRender: true, - scrollY: "80vh", + scrollY: "70vh", scrollX: true, "searching": false, "lengthMenu": [[15, 30, 60, -1], [15, 30, 60, "All"]], @@ -562,16 +559,15 @@

Coverage of Known Variants

scrollY: 500, scrollCollapse: true, scroller: true, - lengthChange: false, columns: columnDefs, columnDefs: [{ - targets: thresholdIdx, - render: function(data, type, row, meta) { - // colours threshold column by value - color = getColor(data) - barSize = 100 - data - return '
' + data + '
'; - } + targets: thresholdIdx, + render: function(data, type, row, meta) { + // colours threshold column by value + color = getColor(data) + barSize = 100 - data + return '
' + data + '
'; + } }] }); }); From e6f83e3a7818dfb77568baa80f762bd4e9493eb1 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Tue, 29 Jun 2021 16:59:03 +0100 Subject: [PATCH 053/100] add multiprocessing to generate low exon plots --- bin/coverage_report_single.py | 66 ++++++++++++++++++++++++----------- 1 file changed, 45 insertions(+), 21 deletions(-) diff --git a/bin/coverage_report_single.py b/bin/coverage_report_single.py index 1b8e248c..d6ff2ba4 100644 --- a/bin/coverage_report_single.py +++ b/bin/coverage_report_single.py @@ -76,20 +76,15 @@ def low_exon_plot(self, low_raw_cov): Returns: - low_exon_plots (str): list of plot values in div tags """ - print("Generating plots of low covered regions") + if len(low_raw_cov.index) == 0: + # empty df passed, likely from difference in total cores and plots + return # get list of tuples of genes and exons to define plots genes = low_raw_cov.drop_duplicates( ["gene", "exon"])[["gene", "exon"]].values.tolist() genes = [tuple(exon) for exon in genes] - if len(genes) == 0: - # everything above threshold, don't generate plots - fig = "

All regions in panel above threshold, no plots\ - to show.

" - - return fig - # sort list of genes/exons by gene and exon genes = sorted(genes, key=lambda element: (element[0], element[1])) @@ -1471,27 +1466,54 @@ def main(): # generate plot of sub optimal regions fig = plots.low_exon_plot(low_raw_cov) - if num_cores == 1: - print("Generating full gene plots") - all_plots = plots.all_gene_plots(raw_coverage) - elif len(cov_summary.index) < int(args.limit) or int(args.limit) == -1: + if len(cov_summary.index) < int(args.limit) or int(args.limit) == -1: # generate plots of each full gene print("Generating full gene plots") + if num_cores == 1: + # specified one core, generate plots slowly + all_plots = plots.all_gene_plots(raw_coverage) + else: + raw_coverage = raw_coverage.sort_values( + ["gene", "exon"], ascending=[True, True] + ) - raw_coverage = raw_coverage.sort_values( - ["gene", "exon"], ascending=[True, True] - ) + # get unique list of genes + genes = raw_coverage.drop_duplicates(["gene"])["gene"].values.tolist() + + # split gene list equally for seperate processes + gene_array = np.array_split(np.array(genes), num_cores) + + # split df into seperate dfs by genes in each list + split_dfs = np.asanyarray( + [raw_coverage[raw_coverage["gene"].isin(x)] for x in gene_array], + dtype=object + ) + + with multiprocessing.Pool(num_cores) as pool: + # use a pool to spawn multiple processes + # uses number of cores defined and splits processing of df + # slices, add each to pool with threshold values + all_plots = pool.map(plots.all_gene_plots, split_dfs) + all_plots = "".join(all_plots) + else: + all_plots = "
Full gene plots have been omitted from this report\ + due to the high number of genes in the panel.
" + + if len(low_raw_cov.index) > 0: + # some low covered regions, generate plots + print("Generating plots of low covered regions") # get unique list of genes - genes = raw_coverage.drop_duplicates(["gene"])["gene"].values.tolist() + genes = low_raw_cov.drop_duplicates(["gene"])["gene"].values.tolist() + print(f"Plots for {len(genes)} to generate") # split gene list equally for seperate processes gene_array = np.array_split(np.array(genes), num_cores) # split df into seperate dfs by genes in each list split_dfs = np.asanyarray( - [raw_coverage[raw_coverage["gene"].isin(x)] for x in gene_array], + [low_raw_cov[low_raw_cov["gene"].isin(x)] for x in gene_array], dtype=object ) @@ -1499,11 +1521,13 @@ def main(): # use a pool to spawn multiple processes # uses number of cores defined and splits processing of df # slices, add each to pool with threshold values - all_plots = pool.map(plots.all_gene_plots, split_dfs) - all_plots = "".join(all_plots) + fig = pool.map(plots.low_exon_plot, split_dfs) + # can return None => remove before joining + fig = [fig_str for fig_str in fig if fig_str] + fig = ",".join(fig) else: - all_plots = "
Full gene plots have been omitted from this report\ - due to the high number of genes in the panel.
" + fig = "

All regions in panel above threshold, no plots\ + to show.

" if args.summary: # summary text to be included From a1e568495c6667c25787a071587ceca7afb2b3b8 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Tue, 29 Jun 2021 17:14:27 +0100 Subject: [PATCH 054/100] change example report in `/data/example` --- data/example/Example_coverage_report.html | 21619 +------------------- 1 file changed, 469 insertions(+), 21150 deletions(-) diff --git a/data/example/Example_coverage_report.html b/data/example/Example_coverage_report.html index c0d224c5..7f9097e5 100644 --- a/data/example/Example_coverage_report.html +++ b/data/example/Example_coverage_report.html @@ -2,7 +2,31 @@ - @@ -79,7 +136,7 @@

Report details

It contains the following sections:
  • Summary including per gene coverage chart.
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  • Table of exons with sub-optimal coverage (<100% coverage at 20x).
    • +
  • Table of exons with sub-optimal coverage (<100% coverage at 50x).
  • Interactive plots of exons with sub-optimal coverage.
  • A summary table of average coverage across all genes.
  • Full gene coverage plots.
    • @@ -98,19 +155,21 @@

    Summary

  • Reference build used for aligment GRCh37 (hs37d5)
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  • Panel(s) / gene(s) included in report: Hydrocephalus
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  • Genes in the applied panel(s): 66
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  • Low coverage threshold: < 20x
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  • Panel coverage at 20x: 99.87 %
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  • Genes with 100% coverage at 20x: 59
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  • Genes not 100% covered at 20x: 7
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  • Genes in the applied panel(s): 15
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  • Low coverage threshold: < 50x
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  • Panel coverage at 50x: 98.56 %
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  • Genes with 100% coverage at 50x: 6
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  • Genes not 100% covered at 50x: 9
  • Clinical report summary:
    • AKT3 (NM_005465.4); AP1S2 (NM_001272071.1); ARSB (NM_000046.3); B3GALNT2 (NM_152490.4); B3GLCT (NM_194318.3); BUB1B (NM_001211.5); CC2D2A (NM_001080522.2); CCDC88C (NM_001080414.3); CCND2 (NM_001759.3); CEP83 (NM_016122.2); COL4A1 (NM_001845.4); CRB2 (NM_173689.5); DAG1 (NM_004393.5); DENND5A (NM_015213.3); DHCR24 (NM_014762.3); EML1 (NM_001008707.1); ERF (NM_006494.2); FAM20C (NM_020223.3); FANCB (NM_001018113.1); FGFR1 (NM_001174067.1); FGFR2 (NM_022970.3); FGFR3 (NM_001163213.1); FKRP (NM_024301.4); FKTN (NM_006731.2); FLVCR2 (NM_017791.2); FMR1 (NM_002024.5); GFAP (NM_002055.4); GLI3 (NM_000168.5); GPSM2 (NM_013296.4); GUSB (NM_000181.3); HYLS1 (NM_001134793.1); IDS (NM_000202.5); ISPD (NM_001101426.3); KIAA1109 (NM_015312.3); L1CAM (NM_000425.4); LAMB1 (NM_002291.2); LARGE1 (NM_004737.4); MAN2B1 (NM_000528.3); NF1 (NM_000267.3); NSD1 (NM_022455.4); OSTM1 (NM_014028.3); PIK3CA (NM_006218.2); PIK3R2 (NM_005027.3); PLG (NM_000301.3); POMGNT1 (NM_001243766.1); POMGNT2 (NM_032806.5); POMK (NM_032237.4); POMT1 (NM_007171.3); POMT2 (NM_013382.5); PPP2R5D (NM_006245.3); PTCH1 (NM_000264.3); PTEN (NM_000314.4); RNF125 (NM_017831.3); RPS6KA3 (NM_004586.2); RXYLT1 (NM_014254.2); SKI (NM_003036.3); SNX10 (NM_001199835.1); STRADA (NM_001003787.2); SUFU (NM_016169.3); SUMF1 (NM_182760.3); TCF12 (NM_207036.1); TWIST1 (NM_000474.3); USP9X (NM_001039590.2); ZBTB20 (NM_001164342.1); ZIC2 (NM_007129.3); ZIC3 (NM_003413.3). -

    99 % of this panel was sequenced to a depth of 20x or + padding-bottom: 15px; padding-top:10px">ADGRG1 (NM_005682.5); ARX (NM_139058.2); CASK (NM_003688.3); DCX (NM_000555.3); DYNC1H1 (NM_001376.4); LAMB1 (NM_002291.2); NDE1 (NM_001143979.1); OCLN (NM_002538.3); PAFAH1B1 (NM_000430.3); RELN (NM_005045.3); TUBA1A (NM_001270399.1); TUBA8 (NM_018943.2); TUBB2B (NM_178012.4); TUBB3 (NM_006086.3); VLDLR (NM_003383.3). +

    Genes with coverage at 50x less than 90%: + ARX (NM_139058.2) 84.07%; OCLN (NM_002538.3) 85.87%. +

    98 % of this panel was sequenced to a depth of 50x or greater.
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    - -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    GeneTranscriptMinMeanMax10x20x30x50x100x
    1AKT3NM_005465.433168.31306100.00100.00100.0098.5986.17
    2AP1S2NM_001272071.10203.8029796.4396.4396.4396.4394.74
    3ARSBNM_000046.350135.32302100.00100.00100.00100.0072.35
    4B3GALNT2NM_152490.426191.01395100.00100.0099.6995.1990.44
    5B3GLCTNM_194318.354141.07267100.00100.00100.00100.0078.68
    6BUB1BNM_001211.546144.20319100.00100.00100.0099.8584.39
    7CC2D2ANM_001080522.246169.47388100.00100.00100.0099.8078.70
    8CCDC88CNM_001080414.361211.51429100.00100.00100.00100.0093.54
    9CCND2NM_001759.385222.94327100.00100.00100.00100.0098.69
    10CEP83NM_016122.261195.34349100.00100.00100.00100.0095.25
    11COL4A1NM_001845.471166.48355100.00100.00100.00100.0088.53
    12CRB2NM_173689.562280.15529100.00100.00100.00100.0096.28
    13DAG1NM_004393.5104303.96500100.00100.00100.00100.00100.00
    14DENND5ANM_015213.340243.86440100.00100.00100.0099.2196.45
    15DHCR24NM_014762.355158.00331100.00100.00100.00100.0086.95
    16EML1NM_001008707.117194.54400100.0099.7498.6897.1894.40
    17ERFNM_006494.26231.3835598.1098.1098.1098.1098.10
    18FAM20CNM_020223.336133.12248100.00100.00100.0097.3565.01
    19FANCBNM_001018113.189215.94332100.00100.00100.00100.0099.43
    20FGFR1NM_001174067.154159.13285100.00100.00100.00100.0088.87
    21FGFR2NM_022970.335144.59276100.00100.00100.0099.6280.82
    22FGFR3NM_001163213.132259.22409100.00100.00100.0098.9995.30
    23FKRPNM_024301.4107209.48414100.00100.00100.00100.00100.00
    24FKTNNM_006731.269168.40288100.00100.00100.00100.0088.75
    25FLVCR2NM_017791.266184.52350100.00100.00100.00100.0093.63
    26FMR1NM_002024.546203.09349100.00100.00100.0098.7494.39
    27GFAPNM_002055.477202.12344100.00100.00100.00100.0094.67
    28GLI3NM_000168.544216.40597100.00100.00100.0099.8792.13
    29GPSM2NM_013296.459188.70316100.00100.00100.00100.0094.48
    30GUSBNM_000181.351174.34363100.00100.00100.00100.0082.56
    31HYLS1NM_001134793.183292.70454100.00100.00100.00100.0092.19
    32IDSNM_000202.567176.18292100.00100.00100.00100.0094.03
    33ISPDNM_001101426.373154.28299100.00100.00100.00100.0087.70
    34KIAA1109NM_015312.361205.02374100.00100.00100.00100.0097.59
    35L1CAMNM_000425.496321.62486100.00100.00100.00100.0099.90
    36LAMB1NM_002291.259212.83365100.00100.00100.00100.0097.61
    37LARGE1NM_004737.445161.56360100.00100.00100.0099.3787.39
    38MAN2B1NM_000528.377201.48371100.00100.00100.00100.0098.53
    39NF1NM_000267.336163.42356100.00100.00100.0099.0082.39
    40NSD1NM_022455.445238.36466100.00100.00100.0099.7395.76
    41OSTM1NM_014028.366160.15267100.00100.00100.00100.0086.10
    42PIK3CANM_006218.263187.39324100.00100.00100.00100.0095.30
    43PIK3R2NM_005027.335218.33379100.00100.00100.0094.8684.21
    44PLGNM_000301.343174.95324100.00100.00100.0099.5483.98
    45POMGNT1NM_001243766.188225.19409100.00100.00100.00100.0098.54
    46POMGNT2NM_032806.557210.02445100.00100.00100.00100.0088.93
    47POMKNM_032237.4197301.84470100.00100.00100.00100.00100.00
    48POMT1NM_007171.363157.90291100.00100.00100.00100.0095.76
    49POMT2NM_013382.577177.91354100.00100.00100.00100.0096.14
    50PPP2R5DNM_006245.3115275.77447100.00100.00100.00100.00100.00
    51PTCH1NM_000264.318177.20428100.0099.9599.6298.7390.59
    52PTENNM_000314.455184.67348100.00100.00100.00100.0089.17
    53RNF125NM_017831.398198.61316100.00100.00100.00100.0099.73
    54RPS6KA3NM_004586.252179.94369100.00100.00100.00100.0090.42
    55RXYLT1NM_014254.280235.04385100.00100.00100.00100.0092.95
    56SKINM_003036.316189.21338100.0099.9599.8697.7487.59
    57SNX10NM_001199835.194161.66248100.00100.00100.00100.0098.79
    58STRADANM_001003787.289179.30327100.00100.00100.00100.0099.36
    59SUFUNM_016169.384168.53275100.00100.00100.00100.0095.36
    60SUMF1NM_182760.394199.19304100.00100.00100.00100.0099.34
    61TCF12NM_207036.189206.88356100.00100.00100.00100.0099.30
    62TWIST1NM_000474.3697.6620697.5790.3087.5674.7949.27
    63USP9XNM_001039590.242211.87476100.00100.00100.0099.4492.70
    64ZBTB20NM_001164342.1125294.26448100.00100.00100.00100.00100.00
    65ZIC2NM_007129.33186.7944694.5393.3088.2183.6076.55
    66ZIC3NM_003413.387244.56372100.00100.00100.00100.0098.32
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    + + + + + + + + + + + + + + + + + +
    GeneTranscriptMinMeanMax10x20x30x50x100x
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    Coverage for all regions of all genes

    + +

    Per exon coverage


    - The following section provides coverage metrics for each exon of each gene.
    - This is a very large table with comprehensive coverage metrics of all target regions. + The following section provides coverage metrics for every exon of each gene.

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    1051ZIC3NM_003413.3X11070136648845136649915115259.27372100.00100.00100.00100.00100.00
    1052ZIC3NM_003413.3X217413665105513665122987142.21170100.00100.00100.00100.0086.20
    1053ZIC3NM_003413.3X3190136652044136652234182255.44295100.00100.00100.00100.00100.00
    - -
    + + + + + + + + + + + + + + + + + + + + + +
    GeneTranscriptChrExonLengthStartEndMinMeanMax10x20x30x50x100x


    @@ -20293,1002 +291,31 @@

    Coverage for all regions of all genes

    Coverage of Known Variants


    - Below are tables giving coverage of known variants. The low coverage table gives those not covered at 20x, - and the high coverage table contains those covered above 20x.

    + Below are tables giving coverage of known variants. The low coverage table gives those not covered at 50x, + and the high coverage table contains those covered above 50x.

    -
  • 88 variants were within the given panel regions and included for analysis
    • -
  • 69 (78.4 %) were covered at or above 20x
    • -
  • 0 (0 %) variants were not covered at 20x
    • -
  • 19 (21.59 %) variants spanned region boundaries
    • +
  • 0 variants were within the given panel regions and included for analysis
    • +
  • 0 (0 %) were covered at or above 50x
    • +
  • 0 (0 %) variants were not covered at 50x
    • +
  • 0 (0 %) variants spanned region boundaries

    • -
    VCF(s) of known variants included in report: hgmd_pro_2020.2_hg38
    -
    - -
    Variants included in the first table below either fully or partially span panel region(s). These are most likely large structural variants and as such do not have coverage data available. See the "info" column for details on the variant.
    -
    Table of variants spanning panel regions(s)   - -
    - -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    VCF Chromosome Position Ref Alt Info
    1hgmd1238856622TDELCLASS=DM;MUT=ALT;SVTYPE=DEL;END=244979216;SVLEN=-6122594;GENE=AKT3;STRAND=-;DNA=NM_005465.4%3Ac.-1136046_*4648626del6122594;PHEN="Developmental_delay%2C_microcephaly%2C_agenesis_of_the_corpus_callosum%2C_epilepsy%2C_language_delay_&_hearing_impairment"
    2hgmd1242100310GDELCLASS=DM;MUT=ALT;SVTYPE=DEL;END=244396370;SVLEN=-2296060;GENE=AKT3;STRAND=-;DNA=NM_005465.4%3Ac.-553200_*1404938del2296060;PHEN="Developmental_delay%2C_microcephaly%2C_and_dysmorphic_features"
    3hgmd34394808TDELCLASS=DM;MUT=ALT;SVTYPE=DEL;END=4835003;SVLEN=-440195;GENE=ITPR1;STRAND=+;DNA=NM_002222.5%3Ac.-98887_7840-1769del440195;PHEN="Spinocerebellar_ataxia_15"
    4hgmd34434022GDELCLASS=DM;MUT=ALT;SVTYPE=DEL;END=4778429;SVLEN=-344407;GENE=ITPR1;STRAND=+;DNA=NM_002222.5%3Ac.-59670_6102+1060del344407;PHEN="Spinocerebellar_ataxia_15/16"
    5hgmd34452827ADELCLASS=DM;MUT=ALT;SVTYPE=DEL;END=4693732;SVLEN=-240905;GENE=ITPR1;STRAND=+;DNA=NM_002222.5%3Ac.-40869_4201del240905;PHEN="Ataxia%2C_adult-onset"
    6hgmd34481881ADELCLASS=DM;MUT=ALT;SVTYPE=DEL;END=4719399;SVLEN=-237518;GENE=ITPR1;STRAND=+;DNA=NM_002222.5%3Ac.-11816_5031+7531del237518;PHEN="Spinocerebellar_ataxia_15"
    7hgmd415563872CDELCLASS=DM;MUT=ALT;SVTYPE=DEL;END=15580017;SVLEN=-16145;GENE=CC2D2A;STRAND=+;DNA=NM_001080522.2%3Ac.3182+355_3825del16145;PROT=NP_001073991.2%3Ap.(Ser1061Argfs*5);PHEN="Rod-cone_dystrophy%2C_non-syndromic"
    8hgmd5176033082TDELCLASS=DM;MUT=ALT;SVTYPE=DEL;END=177973268;SVLEN=-1940186;GENE=NSD1;STRAND=+;DNA=NM_022455.4%3Ac.-1100885_*677811del1940186;PHEN="Sotos_syndrome"
    9hgmd841346127CDELCLASS=DM;MUT=ALT;SVTYPE=DEL;END=43050787;SVLEN=-1704660;GENE=SLC20A2;STRAND=-;DNA=NM_006749.4%3Ac.-509231_*1071675del1704660;PHEN="Primary_familial_brain_calcification"
    10hgmd842481202ADELCLASS=DM;MUT=ALT;SVTYPE=DEL;END=43061742;SVLEN=-580540;GENE=SLC20A2;STRAND=-;DNA=NM_006749.4%3Ac.-520186_-264-8549del580540;PHEN="Primary_familial_brain_calcification"
    11hgmd9134339872ADELCLASS=DM?;MUT=ALT;SVTYPE=DEL;END=136212966;SVLEN=-1873094;GENE=COL5A1;STRAND=+;DNA=NM_000093.4%3Ac.-302315_*1370663del1873094;PHEN="Ehlers-Danlos_syndrome"
    12hgmd1292443578TDELCLASS=DM;MUT=ALT;SVTYPE=DEL;END=95515465;SVLEN=-3071887;GENE=CRADD;STRAND=+;DNA=NM_003805.4%3Ac.-1233900_*1665194del3071887;PHEN="Lissencephaly%2C_thin"
    13hgmd1557186282TDELCLASS=DM;MUT=ALT;SVTYPE=DEL;END=57271231;SVLEN=-84949;GENE=TCF12;STRAND=+;DNA=NM_207036.1%3Ac.391-5871_1746-1795del84949;PROT=NP_996919.1%3Ap.(Ser131Glnfs*3);PHEN="Coronal_craniosynostosis"
    14hgmd1910164297CDELCLASS=DM?;MUT=ALT;SVTYPE=DEL;END=13197574;SVLEN=-3033277;GENE=KLF1;STRAND=-;DNA=NM_006563.4%3Ac.-310434_*2720587del3033277;PHEN="Hereditary_persistence_of_foetal_haemoglobin"
    15hgmd1912469611ADELCLASS=DM?;MUT=ALT;SVTYPE=DEL;END=13919918;SVLEN=-1450307;GENE=KLF1;STRAND=-;DNA=NM_006563.4%3Ac.-1032778_*415273del1450307;PHEN="Hereditary_persistence_of_foetal_haemoglobin"
    16hgmdX136621442GDELCLASS=DM;MUT=ALT;SVTYPE=DEL;END=136655378;SVLEN=-33936;GENE=CD40LG;STRAND=+;DNA=NM_000074.2%3Ac.-26806_346+948del33936;PHEN="Hyper-IgM_syndrome"
    17hgmdX136622040TDELCLASS=DM;MUT=ALT;SVTYPE=DEL;END=136678334;SVLEN=-56294;GENE=CD40LG;STRAND=+;DNA=NM_000074.2%3Ac.-26208_*18919del56294;PHEN="Hyper-IgM_syndrome"
    18hgmdX136643745TDELCLASS=DM;MUT=ALT;SVTYPE=DEL;END=136649114;SVLEN=-5369;GENE=CD40LG;STRAND=+;DNA=NM_000074.2%3Ac.-4500_156+713del5369;PHEN="Hyper-IgM_syndrome"
    19hgmdX20204020ADELCLASS=DM;MUT=ALT;SVTYPE=DEL;END=20209403;SVLEN=-5383;GENE=RPS6KA3;STRAND=-;DNA=NM_004586.2%3Ac.128_325+1del5383;PROT=NP_004577.1%3Ap.(Glu43_Lys108del);PHEN="Coffin-Lowry_syndrome"
    - -

    + - Table of variants with low coverage (< 20x)   + Table of variants with low coverage (< 50x)  
    - No low covered SNPs + No variants with coverage < 50x

    - Table of variants with high coverage (>= 20x)   + Table of variants with high coverage (>= 50x)  
    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    VCF Gene Exon Chromosome Position Ref Alt Coverage
    1hgmdARSB5578181545TA142
    2hgmdCC2D2A27415569340ATGTA212
    3hgmdCC2D2A27415569345GTGTG218
    4hgmdCC2D2A27415569346TC219
    5hgmdCC2D2A32415587838GT166
    6hgmdCC2D2A37415601264TC140
    7hgmdCC2D2A37415601291GCTGTGTATA131
    8hgmdCC2D2A37415601303AG128
    9hgmdCC2D2A37415601328CG109
    10hgmdFAM20C17193649GGC81
    11hgmdFAM20C17193671GCG82
    12hgmdFAM20C27195624TA198
    13hgmdFAM20C27195721TA142
    14hgmdFAM20C27195737GC133
    15hgmdFAM20C37208916CT120
    16hgmdFAM20C37208951GA138
    17hgmdFGFR3441801519CT158
    18hgmdFGFR3741803731CG152
    19hgmdFGFR3741803732TA152
    20hgmdFGFR3741803744AT119
    21hgmdFGFR3741803746GA107
    22hgmdFGFR3941806076GA132
    23hgmdFGFR3941806096GA162
    24hgmdFGFR3941806162AC183
    25hgmdFGFR3941806162AG183
    26hgmdFGFR3941806162AAGAATGC183
    27hgmdFGFR3941806163AC184
    28hgmdFGFR3941806163AT184
    29hgmdFGFR3941806164GC187
    30hgmdFGFR3941806164GT187
    31hgmdFGFR31141807189CAGC286
    32hgmdNF1281729562625CT94
    33hgmdPPP2R5D5642975006GTG300
    34hgmdPPP2R5D5642975040TC276
    35hgmdPPP2R5D13642978268CT247
    36hgmdPPP2R5D13642978283CTC278
    37hgmdPPP2R5D13642978294AGA260
    38hgmdPPP2R5D13642978298GC252
    39hgmdPPP2R5D14642978406AT258
    40hgmdPPP2R5D14642978424GA262
    41hgmdPPP2R5D14642978460ACTA239
    42hgmdPPP2R5D14642978460AACT239
    43hgmdPPP2R5D15642978620TGT422
    44hgmdPPP2R5D15642978633CTC403
    45hgmdPPP2R5D15642978640CCA407
    46hgmdPPP2R5D15642978663CG370
    47hgmdPPP2R5D16642978903AG363
    48hgmdPPP2R5D16642978926CCA406
    49hgmdPPP2R5D16642978981AG400
    50hgmdRPS6KA311X20195115CG254
    51hgmdRPS6KA311X20195118TC254
    52hgmdRPS6KA311X20195128TA247
    53hgmdRPS6KA311X20195131GA229
    54hgmdRPS6KA311X20195137GA225
    55hgmdRPS6KA311X20195143GA225
    56hgmdRPS6KA311X20195146CG223
    57hgmdRPS6KA311X20195156TC217
    58hgmdSTRADA131761780974GC139
    59hgmdSTRADA131761780979AG150
    60hgmdSTRADA131761780982GT153
    61hgmdSTRADA131761780991TC161
    62hgmdSUMF1834418009CG255
    63hgmdSUMF1834418029GA265
    64hgmdSUMF1834418033GC263
    65hgmdSUMF1834418043CCA261
    66hgmdSUMF1834418046TC256
    67hgmdSUMF1834418065GA252
    68hgmdSUMF1834418073GCG249
    69hgmdTCF12101557524632CA286
    + No variants covered at 50x/b>


    @@ -21296,17 +323,231 @@

    Coverage of Known Variants

    -    Report generated on 2020-11-16 +    Report generated on 2021-06-29 Report created with Athena -
    +
    + + + + + + + + + + + + + + + + + + + - - + + + + + +
- - \ No newline at end of file + From efb56a35d230cd4356ae0883cd1007e017c70dd0 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Tue, 29 Jun 2021 17:16:31 +0100 Subject: [PATCH 055/100] remove old arg --- bin/coverage_report_single.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/coverage_report_single.py b/bin/coverage_report_single.py index d6ff2ba4..e4c68f2b 100644 --- a/bin/coverage_report_single.py +++ b/bin/coverage_report_single.py @@ -71,7 +71,6 @@ def low_exon_plot(self, low_raw_cov): Args: - low_raw_cov (df): df of raw coverage for exons with low coverage - - threshold (int): defined threshold level (default: 20) Returns: - low_exon_plots (str): list of plot values in div tags @@ -1522,6 +1521,7 @@ def main(): # uses number of cores defined and splits processing of df # slices, add each to pool with threshold values fig = pool.map(plots.low_exon_plot, split_dfs) + # can return None => remove before joining fig = [fig_str for fig_str in fig if fig_str] fig = ",".join(fig) From 37bdf292d437dbed1ea0a0c3050f7cf7043dee31 Mon Sep 17 00:00:00 2001 From: jethror1 <45037268+jethror1@users.noreply.github.com> Date: Tue, 29 Jun 2021 17:34:39 +0100 Subject: [PATCH 056/100] remove ws --- data/templates/single_template.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/templates/single_template.html b/data/templates/single_template.html index 271cc324..7a6459ef 100644 --- a/data/templates/single_template.html +++ b/data/templates/single_template.html @@ -187,7 +187,7 @@

Exons with <100% coverage at $threshold

- + From 9e8f0fa07d865361236016afb1ddd04fd66450d2 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Tue, 29 Jun 2021 18:28:57 +0100 Subject: [PATCH 057/100] changes to summary text: - added max height of 500px, becomes scrollable div beyond for large panels - moved copy to clipboard button to template --- bin/coverage_report_single.py | 25 ++++++++++--------------- data/templates/single_template.html | 6 ++++++ 2 files changed, 16 insertions(+), 15 deletions(-) diff --git a/bin/coverage_report_single.py b/bin/coverage_report_single.py index e4c68f2b..fa986ff7 100644 --- a/bin/coverage_report_single.py +++ b/bin/coverage_report_single.py @@ -997,8 +997,8 @@ def write_summary(self, cov_summary, threshold, panel_pct_coverage): summary_text = """
  • Clinical report summary:
    • -
    """ sub90 = "" @@ -1024,20 +1024,15 @@ def write_summary(self, cov_summary, threshold, panel_pct_coverage): else: sub90 = sub90.strip(" ;") + "." - summary_text += """ -

    Genes with coverage at {} less than 90%: - {}""".format(self.threshold, sub90) - - summary_text += """ -

    {} % of this panel was sequenced to a depth of {} or - greater.
    """.format(pct_cov, self.threshold) + summary_text += ( + f"

    Genes with coverage at {self.threshold} " + f"less than 90%: {sub90}" + ) - # add closing div and copy button for summary text - summary_text += """
    -
    """ + summary_text += ( + f"

    {pct_cov} % of this panel was sequenced to a depth " + f"of {self.threshold} or greater.
    " + ) return summary_text diff --git a/data/templates/single_template.html b/data/templates/single_template.html index 271cc324..d628d76b 100644 --- a/data/templates/single_template.html +++ b/data/templates/single_template.html @@ -155,6 +155,12 @@

    Summary

  • Genes with 100% coverage at $threshold: $fully_covered_genes
  • Genes not 100% covered at $threshold: $gene_issues
    • $summary_text +
    + +
    $summary_plot From 3f68a92a079aff97ddebe0cded4db0107607dc1d Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Tue, 29 Jun 2021 22:12:50 +0100 Subject: [PATCH 058/100] improve low exon threshold column colouring for nicer colours --- data/templates/single_template.html | 24 +++++++++++++++++------- 1 file changed, 17 insertions(+), 7 deletions(-) diff --git a/data/templates/single_template.html b/data/templates/single_template.html index 1684436a..4c5a9031 100644 --- a/data/templates/single_template.html +++ b/data/templates/single_template.html @@ -536,13 +536,23 @@

    Coverage of Known Variants

    + + + + + + + + + + + + From 2bfe57f273db6ffc9c96072ecdf55fa9b67b7398 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Mon, 5 Jul 2021 12:00:09 +0100 Subject: [PATCH 082/100] add horizontal seperators --- data/templates/single_template.html | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/data/templates/single_template.html b/data/templates/single_template.html index 097f329f..70be8a05 100644 --- a/data/templates/single_template.html +++ b/data/templates/single_template.html @@ -165,7 +165,7 @@

    Summary

    $summary_plot -



    +



    Exons with <100% coverage at $threshold

    @@ -198,7 +198,7 @@

    Exons with <100% coverage at $threshold

    -



    +



    @@ -230,10 +230,10 @@

    Per gene coverage summary

    -



    +



    - +

    Per exon coverage


    The following section provides coverage metrics for every exon of each gene. @@ -246,7 +246,7 @@

    Per exon coverage

    -

    +

    @@ -259,8 +259,8 @@

    Coverage of Known Variants

  • $snps_covered ($snps_pct_covered %) were covered at or above $threshold
  • $snps_not_covered ($snps_pct_not_covered %) variants were not covered at $threshold
  • $snps_out_panel ($snps_pct_out_panel %) variants spanned region boundaries
    • - $vcfs -
    +
  • $vcfs
    • +

    @@ -281,7 +281,7 @@

    Coverage of Known Variants

    -

    +

    @@ -318,7 +318,7 @@

    Coverage of Known Variants

    --> -

    +

    Table of variants with high coverage (>= $threshold)   @@ -762,7 +762,6 @@

    Coverage of Known Variants

    } ); - - @@ -556,6 +560,16 @@

    Coverage of Known Variants

    } + + + + + + + + + + + + + + - - - - - - - - - - - + @@ -354,7 +354,7 @@

    Coverage of Known Variants

    // $exon_issues is int passed from report script var exon_check = $exon_issues if (exon_check == 0) { - document.getElementById('low_exon_plots').style.display = "none"; + document.getElementById('low_exon_plots').style.display = "none"; } @@ -367,11 +367,12 @@

    Coverage of Known Variants

    for (i = 0; i < coll.length; i++) { coll[i].addEventListener("click", function() { this.classList.toggle("active"); + var content = this.nextElementSibling; - if (content.style.maxHeight){ - content.style.maxHeight = null; + if (content.style.maxHeight) { + content.style.maxHeight = null; } else { - content.style.maxHeight = content.scrollHeight * 2 + "px"; + content.style.maxHeight = content.scrollHeight * 2 + "px"; } }); } From 228985fd5068d83d32097a23e1c230f7bd402208 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Tue, 6 Jul 2021 11:47:02 +0100 Subject: [PATCH 092/100] fix rounding for sub-threshold table --- bin/coverage_report_single.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/bin/coverage_report_single.py b/bin/coverage_report_single.py index eadd3bc9..bf43c309 100644 --- a/bin/coverage_report_single.py +++ b/bin/coverage_report_single.py @@ -485,7 +485,7 @@ def style_sub_threshold(self): for col in self.threshold_cols: # add dtype for threshold columns - dtypes[col] = int + dtypes[col] = float sub_threshold = pd.DataFrame(columns=column) sub_threshold.astype(dtype=dtypes) @@ -528,14 +528,14 @@ def style_sub_threshold(self): # add index as column to have numbered rows in report sub_threshold_stats.insert(0, ' ', sub_threshold_stats.index) - # make dict for rounding coverage columns to 2dp - rnd = {} - for col in list(sub_threshold_stats.columns[10:]): - rnd[col] = '{0:.2f}%' + round_cols = ['Mean'] + self.threshold_cols - sub_threshold_stats["Mean"] = sub_threshold_stats["Mean"].apply( - lambda x: int(x) - ) + # limit to 2dp using math.floor, use of round() with + # 2dp may lead to inaccuracy such as 99.99 => 100.00 + for col in round_cols: + sub_threshold_stats[col] = sub_threshold_stats[col].map( + lambda col: math.floor(col * 100) / 100 + ) # generate list of dicts with column headers for styling low_exon_columns = [] From bebb5dfda0ca08ffda717185fbd35f88533b1ca0 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Tue, 6 Jul 2021 12:38:37 +0100 Subject: [PATCH 093/100] add comment for clarity --- bin/coverage_report_single.py | 1 + 1 file changed, 1 insertion(+) diff --git a/bin/coverage_report_single.py b/bin/coverage_report_single.py index bf43c309..877a1f0c 100644 --- a/bin/coverage_report_single.py +++ b/bin/coverage_report_single.py @@ -528,6 +528,7 @@ def style_sub_threshold(self): # add index as column to have numbered rows in report sub_threshold_stats.insert(0, ' ', sub_threshold_stats.index) + # list of threshold columns + mean round_cols = ['Mean'] + self.threshold_cols # limit to 2dp using math.floor, use of round() with From 4d667b6e573b150791c85c78b0ff635cc839cbb5 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Tue, 6 Jul 2021 12:46:38 +0100 Subject: [PATCH 094/100] switch mean column to float in sub-threshold table --- bin/coverage_report_single.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/coverage_report_single.py b/bin/coverage_report_single.py index 877a1f0c..89948dad 100644 --- a/bin/coverage_report_single.py +++ b/bin/coverage_report_single.py @@ -479,7 +479,7 @@ def style_sub_threshold(self): dtypes = { 'gene': str, 'tx': str, 'chrom': str, 'exon': int, 'exon_len': int, - 'exon_start': int, 'exon_end': int, 'min': int, 'mean': int, + 'exon_start': int, 'exon_end': int, 'min': int, 'mean': float, 'max': int } From 5cb31a36be9aa436ab84d7e82b8e379877620823 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Tue, 6 Jul 2021 13:19:20 +0100 Subject: [PATCH 095/100] better comment, add type hints --- bin/coverage_report_single.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/bin/coverage_report_single.py b/bin/coverage_report_single.py index 89948dad..fccd95d6 100644 --- a/bin/coverage_report_single.py +++ b/bin/coverage_report_single.py @@ -436,7 +436,10 @@ def summary_gene_plot(self, cov_summary): class styleTables(): """Functions for styling tables for displaying in report""" - def __init__(self, cov_stats, cov_summary, threshold, threshold_cols, vals): + def __init__( + self, cov_stats: pd.DataFrame, cov_summary: pd.DataFrame, + threshold: str, threshold_cols: list, vals: list + ) -> None: self.cov_stats = cov_stats self.cov_summary = cov_summary self.threshold = threshold @@ -461,10 +464,6 @@ def style_sub_threshold(self): """ Styling of sub threshold stats df for displaying in report - Args: - - cov_stats (df): df of per exon coverage stats - - threshold (str): low coverage threshold value - - threshold_cols (list): threshold values for coverage Returns: - sub_threshold_stats (list): list of sub threshold coverage stats - low_exon_columns (list): list of column headers for report @@ -528,7 +527,7 @@ def style_sub_threshold(self): # add index as column to have numbered rows in report sub_threshold_stats.insert(0, ' ', sub_threshold_stats.index) - # list of threshold columns + mean + # threshold_cols -> list of strings, add mean to loop over for rounding round_cols = ['Mean'] + self.threshold_cols # limit to 2dp using math.floor, use of round() with From 43f70e077eb28736a20dde5edf427ae498642185 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Wed, 7 Jul 2021 16:04:43 +0100 Subject: [PATCH 096/100] add file formatting to readme --- README.md | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 7639ef5d..c07ef962 100644 --- a/README.md +++ b/README.md @@ -29,6 +29,15 @@ The general workflow for generating the statistics and report is as follows:
    @@ -39,7 +48,7 @@ Expected inputs: ``` -p / --panel_bed : Input panel bed file; must have ONLY the following 4 columns chromosome, start position, end position, gene/transcript --t / --transcript_file : Transcript annotation file, contains required gene and exon information. must have ONLY the following 6 columns: +-t / --transcript_file : Transcript annotation file, contains required gene and exon information. Must have ONLY the following 6 columns: chromosome, start, end, gene, transcript, exon -c / --coverage_file : Per base coverage file (output from mosdepth or similar) From 4cd2dd5d5d093400a0ed83ae4920117f76242791 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Wed, 7 Jul 2021 16:23:29 +0100 Subject: [PATCH 097/100] add link to page for generating transcript file to readme --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index c07ef962..c28fdd26 100644 --- a/README.md +++ b/README.md @@ -37,6 +37,7 @@ As a minimum, Athena requires 3 input files. These are a bed file for the gene p - transcript file: `chromosome start end gene transcript exon` - coverage file: `chromsome start end coverage` +n.b. the process for creating the transcript file may be found [here][transcript-file-url] ### Annotating BED file The BED file containing regions of interest is first required to be annotated with gene, exon and coverage information prior to analysis. This may be done using [BEDtools intersect][bedtools-intersect-url], with a file containing transcript to gene and exon information, and then the per base coverage data. Currently, 100% overlap is required between coordinates in the panel bed file and the transcript annotation file, therefore you must ensure any added flank regions etc. are the same.
    @@ -146,3 +147,4 @@ Any bugs or suggestions for improvements please raise an issue. [mosdepth-url]: https://github.com/brentp/mosdepth [dx-url]: https://github.com/eastgenomics/eggd_athena +[transcript-file-url]: https://cuhbioinformatics.atlassian.net/wiki/spaces/P/pages/2241101840/Generating+transcripts+file+for+Athena From 8b4b7a6b2fff0b4686a625bf9feed795408f26df Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Wed, 7 Jul 2021 16:24:50 +0100 Subject: [PATCH 098/100] tidy readme --- README.md | 7 ------- 1 file changed, 7 deletions(-) diff --git a/README.md b/README.md index c28fdd26..209d9598 100644 --- a/README.md +++ b/README.md @@ -125,13 +125,6 @@ $ python3 bin/coverage_report_single.py --gene_stats output/sample1-exon-coverag ``` -### For development - -Features to be developed: -- Generate run level statistics from multiple samples -- Generate run level report from multiple samples -- Add interactive elements to tables to increase useability (i.e sorting, filtering, searching) - Any bugs or suggestions for improvements please raise an issue. From bd84c056cb3293e2776e30d5c55a5d82a4ca1394 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Wed, 7 Jul 2021 16:41:45 +0100 Subject: [PATCH 099/100] readme typo --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 209d9598..563d98d5 100644 --- a/README.md +++ b/README.md @@ -35,7 +35,7 @@ As a minimum, Athena requires 3 input files. These are a bed file for the gene p - panel bed file: `chromosome start end transcript` - transcript file: `chromosome start end gene transcript exon` -- coverage file: `chromsome start end coverage` +- coverage file: `chromosome start end coverage` n.b. the process for creating the transcript file may be found [here][transcript-file-url] From 5fa65976eced9c977301be223b4a228137af1da2 Mon Sep 17 00:00:00 2001 From: Jethro Rainford Date: Wed, 7 Jul 2021 16:44:14 +0100 Subject: [PATCH 100/100] readme update --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 563d98d5..f8201a5a 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,7 @@ As a minimum, Athena requires 3 input files. These are a bed file for the gene p - transcript file: `chromosome start end gene transcript exon` - coverage file: `chromosome start end coverage` -n.b. the process for creating the transcript file may be found [here][transcript-file-url] +n.b. the process for creating the transcript file may be found [here][transcript-file-url]. ### Annotating BED file The BED file containing regions of interest is first required to be annotated with gene, exon and coverage information prior to analysis. This may be done using [BEDtools intersect][bedtools-intersect-url], with a file containing transcript to gene and exon information, and then the per base coverage data. Currently, 100% overlap is required between coordinates in the panel bed file and the transcript annotation file, therefore you must ensure any added flank regions etc. are the same.